anno_sample_cat: Helper to specify comp_heatmap annotation for categorical...

In david-barnett/microViz: Microbiome Data Analysis and Visualization

Helper to specify comp_heatmap annotation for categorical sample data

Description

Use this as an argument to sampleAnnotation(), which itself is used by comp_heatmap() as sample_anno argument.

Usage

anno_sample_cat(
  var,
  col = distinct_palette(),
  renamer = identity,
  size = grid::unit(5, "mm"),
  legend = TRUE,
  legend_title = "",
  box_col = "white",
  box_lwd = 0.5,
  border_col = NA,
  border_lwd = 1,
  data = NULL,
  samples = NULL,
  which = NULL,
  ...
)

Arguments

var	name of variable to use for annotation data
col	colors vector, at least as long as unique(x), optionally named by x levels
renamer	function to rename levels of variable var
size	width or height as a grid unit object
legend	generate legend for this annotation (attached as attribute of heatmap, and not automatically included in plot)
legend_title	title for legend, if drawn
box_col	colour of boxes around individual cells
box_lwd	line width of boxes around individual cells
border_col	colour of border around all cells
border_lwd	line width of border around all cells
data	OPTIONAL phyloseq or psExtra, only set this to override use of same data as in heatmap
samples	OPTIONAL selection vector of sample names, only set this if providing data argument to override default
which	OPTIONAL indicating if it is a 'column' or a 'row' annotation, only set this if providing data argument to override default
...	Arguments passed on to anno_cat x data vector, treated as categorical width grid unit object or NULL height grid unit object or NULL

Value

vector of values

Examples

library("ComplexHeatmap")
data("ibd", package = "microViz")
psq <- ibd
samples <- phyloseq::sample_names(psq)

# makes a function that takes data, taxa and which (at minimum)
fun <- anno_sample_cat(var = "ibd")

# manually specify the prevalence barplot function by giving it data etc.
heatmapAnnoFunction <- fun(data = psq, which = "row", samples = samples)

# draw the barplot without a heatmap, you will never normally do this!
vp <- viewport(width = 0.75, height = 0.75)

grid::grid.newpage()
pushViewport(vp)
draw(heatmapAnnoFunction)
# A legend is attached by default to anno_cat() output, let's plot that.
pushViewport(viewport(x = 0.75))
draw(attr(heatmapAnnoFunction, "Legend"))

# change some options and specify the data up front
grid::grid.newpage()
pushViewport(vp)
anno_sample_cat(
  data = psq, var = "DiseaseState", samples = samples, which = "column",
  size = grid::unit(5, "cm"), col = distinct_palette(pal = "kelly")
) %>%
  draw()

david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.